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Wednesday, October 04, 2006

Bioinformatics: Open Source or Open Access??

I have heard that bioinformatics is ahead of chemoinformatics. However, I discoverd that this is not necessarily the case, while preparing for a homology modeling course I gave this week at the CUBIC. Open Access is really no issue there, with open access journals and many open access databases. But it is different when it comes down to open source software.

Below is a list of bioinformatics programs which are free for academic use, but not open:

And this not even includes the many websites which do not offer the software behind them. And these programs cover several steps in the whole homology modeling process. Open source homology modeling is not possible at this moment :(

But, on the bright side, there are already some open source programs involved too:

6 comments:

Egon, I would those call those applications rather modelling applications than bioinformatics applications. And especially this connection is IMHO still not really bridged with good open source software, because people like to sell every little tool to the pharmaceutical industry ... I just say missing bond orders in PDBs.

I would disagree. The software that's widely used by bioinformaticians (it might be different for structural biology...PROCHECK, etc.) is 95% open source. Here are some examples:- BLAST (by NCBI)- fasta (by Bill Pearson)- clustalw (by Des Higgins)- hmmer (by Sean Eddy)- phylip (by Joe Felsenstein)- emboss package- bioperl perl library- genewise (by Ewan Birney)These are some of the most used programs in bioinformatics, but almost every bioinformatics program published nowadays is open source. This underlines the importance of creating a similar variety of open source tools for cheminformatics, until 95% of cheminformatics software is also open source!

There were two comments on bioinformatics books, which actually pointed to a file sharing website which, I think, illegally shares books. Lot's of books really. But it is illegal, and I disapprove of it. Please don't advertise illegal activities in my blog.

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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!

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